Molecular docking of polysaccharides, which are large, complex carbohydrates, presents unique challenges compared to small molecules due to their size, flexibility, and the presence of multiple hydroxyl groups that can participate in hydrogen bonding. Here’s a general approach and some software recommendations for performing molecular docking with polysaccharides:

Software Recommendations:

Approach for Docking Polysaccharides:

Additional Recommendations:

• Parameterization: Ensure that the force fields and parameters used in your simulations are suitable for carbohydrates.
• Computational Resources: Docking polysaccharides is computationally intensive. Make sure you have access to sufficient computational resources.
• Validation: Validate your docking approach with known structures of carbohydrate-protein complexes if available.
• Expertise: The process of docking large, flexible molecules like polysaccharides often requires a deep understanding of both the software and the biological system. Collaboration with experts in computational biology or bioinformatics can be beneficial.

Keep in mind that molecular docking is a complex process with many variables, and it often requires iterative refinement and validation to obtain reliable results.

Zhi Cao Thank you very much. Appreciate it.

We used autodock tools to dock scFv with trissacharide antigen. Docking was followed by MD simulation on gromacs using amber forcefield for scfv and glycam06j forcefield using acpype tool of AmberTools for carbohydrate.

Glycam webserver was used for building carbohydrate structure.

For docking polysaccharides, consider using AutoDock or Dock as they can handle larger, flexible molecules. You may also try GOLD or FlexX. Use AMBER or CHARMM force fields for appropriate parametrization of the polysaccharide and protein interactions.

All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.